I know when creating a league you have the option to load a custom schedule, but is it possible to create a custom schedule each year thereafter? and when/how would you do it?

And in the custom schedule, is it possible when customizing to have a conf (ie Pac12) play 9 conf games, or is it going to blow something up trying to do so?

Yes....when you use a custom schedule, whether during league creation or during the "New Season" phase, that schedule will forever be used until you re-import another schedule. During thew "New Season" phase, you can go into the League Office screen and select the option in the right of the screen to Import a Schedule.

Developers can correct me, but I "think" you can physically create any schedule you want but the custom schedule file must ensure that every team plays 12 games as I believe the import feature checks for the total games included and ensures they occur between week 1 and week 16 in the schedule file. Although even if it doesn't blow up during the import phase, not sure what an unrealistic schedule might do to any of the features of the game, if any. Although I have created a custom schedule for the Pro game, never tried with the College game as I suspected it might be quite a chore getting it right with that many teams to worry about.